The Holmes set is really it's own beast. It's halfway between OD&D and AD&D, with a few odd rules that are unique to to it... Basing initiative on Dexterity, the 5-prong alignment chart, etc.
The B/X and the BE portion of BECMI, are pretty much identical, a few different spells, a couple diferences in the saving throw charts, not much else different. Most of the difference are at 7th level or higher. The only real difference in the Basic rules were presentation, with the 1981 rules being concise and straightforward, and the 1983 rules being a tutorial walk through.
Of course, the CMI portion of BECMI contains all sorts of things that weren't in the BX game, not all of them just high level stuff. Depending on to what extent you integrate things like the Mystics and other new classes, Weapon Skills, demi-human attack ranks, the Immortal rules, and so on, into your low-level game, you may have a very different beast from B/X.
The Rules Cyclopedia is basically a compilation of the BECM portion of BECMI. It has most, but not all of the first four boxes. It also has a number of things that were introduced in the Gazetteer series. Most notably, the Non-Weapon Skills. But also things like a more detailed spell research system.
Really, it's all nitpicking. You're going to be able to use anything for D&D written in 1991 for the 1977 set and vice versa.
For being comprehensive, you'd want the RC, even though there are things in it that I think are poorly written (the combat rules), and a lot of stuff that I, personally, would never use in my game. If you're looking for a nice concise well-written set of rules, either the Holmes (1977) or Moldvay (1981) rules will do. And then use the 1981 Cook Expert rules to continue on past 3rd level. (The Cook rules have an opening note for conversion from the Holmes set.) I think the 1983 Mentzer set is best for people who have no familiarity with rpg's at all. It's too scattered to be a good reference for my taste.